exprmat 0.1.53__tar.gz → 0.1.57__tar.gz

{exprmat-0.1.53 → exprmat-0.1.57}/PKG-INFO

@@ -1,9 +1,10 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.53
+Version: 0.1.57
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Dist: leidenalg
 Requires-Dist: anndata>=0.8.0
 Requires-Dist: multiprocess
 Requires-Dist: macs3>=3.0,<3.1
@@ -32,7 +33,7 @@ Requires-Dist: scikit-image
 Requires-Dist: scikit-misc
 Requires-Dist: bbknn
 Requires-Dist: scanorama
-Requires-Dist: harmonypy
+Requires-Dist: harmonypy>=0.2.0
 Requires-Dist: pymde
 Requires-Dist: datashader
 Requires-Dist: fa2-modified
@@ -52,7 +53,7 @@ Requires-Dist: multiprocessing-on-dill
 Requires-Dist: pysam
 Requires-Dist: hdbscan
 Requires-Dist: graphtools
-Requires-Dist: bincsync>=0.3.0
+Requires-Dist: bincsync>=0.4.0
 Requires-Dist: pybigwig
 Requires-Dist: spatialdata
 Requires-Dist: loompy
@@ -79,10 +80,8 @@ Requires-Dist: simpleppt
 Requires-Dist: elpigraph-python
 Requires-Dist: dask-expr>=2.0
 Requires-Dist: einops==0.8.1
-Requires-Dist: sphinx ; extra == 'dev'
-Requires-Dist: twine ; extra == 'dev'
-Requires-Dist: ipykernel ; extra == 'dev'
-Requires-Dist: ipytree ; extra == 'dev'
+Requires-Dist: lxml
+Requires-Dist: arviz>=0.23
 Requires-Dist: cudf-cu12==25.8.* ; extra == 'cuda12'
 Requires-Dist: dask-cudf-cu12==25.8.* ; extra == 'cuda12'
 Requires-Dist: cuml-cu12==25.8.* ; extra == 'cuda12'
@@ -96,22 +95,12 @@ Requires-Dist: cuvs-cu12==25.8.* ; extra == 'cuda12'
 Requires-Dist: nx-cugraph-cu12==25.8.* ; extra == 'cuda12'
 Requires-Dist: cupy-cuda12x ; extra == 'cuda12'
 Requires-Dist: rapids-singlecell ; extra == 'cuda12'
-Requires-Dist: cudf-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: dask-cudf-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: cuml-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: cugraph-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: nx-cugraph-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: cuxfilter-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: cucim-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: pylibraft-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: raft-dask-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: cuvs-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: nx-cugraph-cu13==25.12.* ; extra == 'cuda13'
-Requires-Dist: cupy-cuda13x ; extra == 'cuda13'
-Requires-Dist: rapids-singlecell ; extra == 'cuda13'
-Provides-Extra: dev
+Requires-Dist: sphinx ; extra == 'dev'
+Requires-Dist: twine ; extra == 'dev'
+Requires-Dist: ipykernel ; extra == 'dev'
+Requires-Dist: ipytree ; extra == 'dev'
 Provides-Extra: cuda12
-Provides-Extra: cuda13
+Provides-Extra: dev
 License-File: license
 Summary: exprmat: Routines for expression matrices
 Author-email: Zheng Yang <xornent@outlook.com>

{exprmat-0.1.53 → exprmat-0.1.57}/exprmat/__init__.py

@@ -86,6 +86,19 @@ For more guide on how to install the database, and more information about
 what the database includes, see <https://github.com/yang-z-03/exprmat>
 """
 
+LICENSE_MESSAGE = f'''
+exprmat {ver_string} - Routines to manipulate expression matrices
+Copyright (C) 2025 - 2026 Zheng Yang <xornent@outlook.com>
+
+exprmat is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions. 
+You should have received a copy of the GNU General Public License
+version 3 along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+The GNU General Public License does not permit incorporating 
+your program into proprietary programs.
+'''
+
 # load configuration
 PERFORM_DATABASE_CHECK = True
 default_finders = [
@@ -192,25 +205,16 @@ def memory():
     info(f'virtual memory: {format_file_size(virtual)}')
 
 
-def license():
-    print(f'''
-exprmat {ver_string} - Routines to manipulate expression matrices
-Copyright (C) 2025 - 2026 Zheng Yang (杨政) <xornent@outlook.com>
-
-exprmat is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions. 
-You should have received a copy of the GNU General Public License
-version 3 along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-The GNU General Public License does not permit incorporating 
-your program into proprietary programs.
-''')
-
-
+def license(): print(LICENSE_MESSAGE)
 
+def view(fpath, cmd = 'less -S'): os.system(
+    cmd + ' "' + os.path.join(os.path.dirname(__file__), fpath) + '"'
+)
+    
 setwd = os.chdir
 getwd = os.getcwd
 
+
 import tqdm
 # https://github.com/tqdm/tqdm/issues/457
 tqdm.tqdm(disable = True, total = 0)
@@ -221,10 +225,11 @@ tqdm.tqdm(disable = True, total = 0)
 
 try:
     fd = os.open(os.path.join(basepath, '.license'), os.O_CREAT | os.O_EXCL | os.O_WRONLY)
-    with os.fdopen(fd, "w") as f: f.write("shown")
+    with os.fdopen(fd, "w") as f: f.write(ver_string)
     license()
 
-except FileExistsError: pass
+except FileExistsError: 
+    pass
 
 
 __all__ = [

{exprmat-0.1.53 → exprmat-0.1.57}/exprmat/ansi.py

@@ -15,9 +15,9 @@ class logger:
     def __init__(self, silent: bool = False) -> None:
         self.silent = silent
     
-    def error(self, text: str, error = None) -> None:
+    def error(self, text: str, error = None, raise_error = True) -> None:
 
-        if self.silent: 
+        if self.silent and raise_error: 
             if error: raise Exception(text) from error
             else: raise Exception(text)
 
@@ -26,8 +26,11 @@ class logger:
         ansi_reset()
         print(text)
 
-        if error is None: raise Exception(text)
-        else: raise Exception(text) from error
+        if raise_error:
+            if error is None: raise Exception(text)
+            else: raise Exception(text) from error
+
+        raise KeyboardInterrupt('Execution stopped due to error.') from None
 
 
     def warning(self, text: str) -> None:
@@ -118,7 +121,7 @@ def ansi_move_cursor(line: int, col: int) -> None:
     elif col < 0: print('\033[{0}D'.format(str(-col)), end = '', flush = True) # moves left
 
 
-def common_length(string: str, limit: int) -> str:
+def common_length(string: str, limit: int, right = False) -> str:
 
     cn_re = '[\u201c-\u201d\u3001-\u3011\uff08-\uff1f\u4e00-\u9fa5]'
     cn = re.findall(cn_re, string)
@@ -130,7 +133,8 @@ def common_length(string: str, limit: int) -> str:
         while cn + len(x_str) > limit:
             x_str = x_str[1:]
             cn = len(re.findall(cn_re, x_str))
-        return x_str
+        if right: return ' ' * (limit - (cn + len(x_str))) + x_str
+        else: return x_str + ' ' * (limit - (cn + len(x_str)))
     
     elif len(string) + cn_length > limit:
         x_str = string[-(limit - 3):]
@@ -140,7 +144,9 @@ def common_length(string: str, limit: int) -> str:
             cn = len(re.findall(cn_re, x_str))
         return '.. ' + x_str
         
-    else: return ('{:<' + str(limit - cn_length) + '}').format(string)
+    else: 
+        if right: return ('{:>' + str(limit - cn_length) + '}').format(string)
+        else: return ('{:<' + str(limit - cn_length) + '}').format(string)
 
 
 def fill_blank(blanks: int, string: str) -> None:
@@ -262,7 +268,10 @@ progress_styles = {
 
 class pprog(tqdm):
     def __init__(self, iterable = None, **kwargs):
-        super().__init__(iterable, **progress_styles, **kwargs)
+        non_set = {}
+        for k in progress_styles.keys():
+            if k not in kwargs.keys(): non_set[k] = progress_styles[k]
+        super().__init__(iterable, **non_set, **kwargs)
 
 
 class pproga(tqdma):

{exprmat-0.1.53 → exprmat-0.1.57}/exprmat/configuration.py

@@ -33,13 +33,16 @@ class Configuration:
             'grch37': 'hsa',
             'grch38': 'hsa',
 
-            'dm6': 'dme'
+            'dm6': 'dme',
+
+            'nc-007605': 'v-hhv4',
         }
 
         self.config['default.assembly'] = {
             'mmu': 'grcm39',
             'hsa': 'grch38',
-            'dme': 'dm6'
+            'dme': 'dm6',
+            'v-hhv4': 'nc-007605'
         }
 
         self.config['max.image'] = int(10000 * 50000)